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Multiple Functionalities of Reduced Flavin in the Non-Redox Reaction

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Multiple Functionalities of Reduced Flavin in the Non-Redox Reaction Archives of Biochemistry and Biophysics 632 (2017) 59e65 Contents lists available at ScienceDirect Archives of Biochemistry and Biophysics journal homepage: www.elsevier.com/locate/yabbi Review article Multiple functionalities of reduced flavin in the non-redox reaction catalyzed by UDP-galactopyranose mutase * ** Pablo Sobrado a, , John J. Tanner b, a Department of Biochemistry, Virginia Tech, Blacksburg, VA 24061, USA b Departments of Biochemistry and Chemistry, University of Missouri, Columbia, MO 65211, USA article info abstract Article history: Flavin cofactors are widely used by enzymes to catalyze a broad range of chemical reactions. Tradi- Received 2 June 2017 tionally, flavins in enzymes are regarded as redox centers, which enable enzymes to catalyze the Received in revised form oxidation or reduction of substrates. However, a new class of flavoenzyme has emerged over the past 21 June 2017 quarter century in which the flavin functions as a catalytic center in a non-redox reaction. Here we Accepted 22 June 2017 introduce the unifying concept of flavin hot spots to understand and categorize the mechanisms and Available online 24 June 2017 reactivities of both traditional and noncanonical flavoenzymes. The major hot spots of reactivity include the N5, C4a, and C4O atoms of the isoalloxazine, and the 20 hydroxyl of the ribityl chain. The role of hot Keywords: fl fl Flavin-dependent reaction spots in traditional avoenzymes, such as monooxygenases, is brie y reviewed. A more detailed fl fl Flavin adducts description of avin hot spots in noncanonical avoenzymes is provided, with a focus on UDP- Galactofuranose galactopyranose mutase, where the N5 functions as a nucleophile that attacks the anomeric carbon Non-redox reaction atom of the substrate. Recent results from mechanistic enzymology, kinetic crystallography, and Neglected diseases computational chemistry provide a complete picture of the chemical mechanism of UDP- Tuberculosis galactopyranose mutase. Redox-switch © 2017 Elsevier Inc. All rights reserved. Conformational changes Protein dynamics Contents 1. Introduction . ................................................. 59 2. Formation of flavin N5-adducts . ............................................ 60 3. Priming the flavin-N5 for reactivity in non-redox reactions . .................................... 61 4. Activation of intermediates in catalysis: role of the flavin-C4O in proton transfer . ..................... 62 5. Summary and outlook . ................................................. 62 Acknowledgments . ........................64 References................................................................. ................................ ........................64 1. Introduction leverage amino acid functional groups to catalyze chemical re- actions [1]. Three-dimensional constellations of amino acids opti- Enzymes exhibit extraordinary catalytic power and diversity, mized by evolution are capable of catalyzing diverse reactions, which remains unmatched by man-made catalysts. All enzymes including phosphoryl transfer, peptide bond hydrolysis, and isom- erization reactions among many others [2e4]. Cofactors expand the chemical repertoire of enzymes, allowing more complex chemical * Corresponding author. reactions to occur. For example, heme-dependent enzymes can ** Corresponding author. cleave C-H bonds via the formation of Fe-oxo species [5]. Pyridoxal E-mail addresses: [email protected] (P. Sobrado), [email protected] phosphate-dependent enzymes form a covalent aldimine (J.J. Tanner). http://dx.doi.org/10.1016/j.abb.2017.06.015 0003-9861/© 2017 Elsevier Inc. All rights reserved. 60 P. Sobrado, J.J. Tanner / Archives of Biochemistry and Biophysics 632 (2017) 59e65 intermediate that facilitates a-C-H bond cleavage, which is impor- 2. Formation of flavin N5-adducts tant in racemization and elimination reactions [6]. Numerous oxi- doreductases use nicotinamide adenine dinucleotide cofactors in The reactivity of the N5-atom of the isoalloxazine ring was hydride transfer reactions. Photosynthetic reaction centers perhaps originally investigated in model compounds where the spectral and represent the pinnacle of cofactor-assisted catalysis [7]. fluorescent properties of N5-alkylated flavins were reported [17,18]. Flavin cofactors are also widely used by enzymes to catalyze a The presence of N5-flavin adducts in enzymes was demonstrated in broad range of chemical reactions. Flavins are derived from ribo- the reaction of D-amino acid oxidase with a nitroethane anion flavin (vitamin B2) and are processed into flavin mononucleotide (Scheme 2) in the presence of cyanide and lactate oxidase with (FMN) or flavin adenine dinucleotide (FAD) in the cell [8]. Typically, glycolate [19]. It was later demonstrated that an N5-adduct played a flavoenzymes catalyze oxidation-reduction reactions, where the role in the catalytic cycle of nitroalkane oxidase [20]. This adduct flavin cycles between the oxidized and reduced states, such as in was later trapped with cyanide and the structure elucidated by x- hydride transfer reactions. In other redox reactions, flavoenzymes ray crystallography [21]. N5-adducts have also been proposed in form a transient semiquinone, such as in electron transfer reactions the reaction of monoamine oxidase with several substrates and [8e12]. inhibitors [22]. The b-Cl-elimination activity of D-amino acid oxi- The isoalloxazine ring of the flavin contains several reactive dase has been proposed to occur via formation of a transient N5- centers or “hot spots” that play important roles in catalysis. In re- covalent intermediate [23]. In these examples, after the initial actions catalyzed by flavin monooxygenases, the activation of ox- attack of the substrate/analogs, formation of a N5-iminium ion or ygen involves a single electron transfer from the reduced flavin and decay of the flavin N5-adduct is coupled to an elimination step (e.g., recombination of the flavin semiquinone with the superoxide ion nitrite, chloride) (Scheme 2). In the N5-iminium ion, a carbon atom forming a covalent intermediate at the C4a-atom, the C4a- is activated for nucleophilic attack by a hydroxide ion (or other peroxyflavin (Scheme 1A) [13]. Formation of this intermediate is nucleophile) as part of the catalytic cycle (Scheme 2). Formation of essential for O-O bond cleavage and substrate oxygenation [14,15]. flavin N5-iminium ions in the methyl transfer steps of the reaction Similarly, C4a-thiol covalent intermediates are formed in gluta- catalyzed by flavin-dependent enzymes in thymidylate biosyn- thione reductase reactions and are involved in the mechanism of thesis and tRNA modifications have also been documented [24,25]. light activation by light-, oxygen-, or voltage-sensitive (LOV) do- Formation of prenylated FMN in decarboxylation reactions by mains (Scheme 1B) [16]. ferulic acid decarboxylase, has been proposed to form via N5- In addition to covalent intermediates at the C4a-position of the iminum ion intermediates [26]. More recently, formation of N5- isoalloxazine ring, covalent intermediates involving the flavin N5 oxoammonium ions, which are important for hydroxylation in have also been characterized. Reactivity of the N5-atom was shown enterocin biosynthesis and in dibenzothiophene degradation, have using model compounds and oxidized flavoenzymes reacting with been proposed [27,28]. These reactions result in reduction of the cabanions (Scheme 1B) [17e19]. Our group and others demon- flavin and oxidation of the substrate/analog. Thus, the flavin must strated the role of a covalent flavin N5 intermediate (Scheme 1A) in cycle back to the oxidized state for sustained catalysis. the isomerization of UDP-galactopyranose (UDP-Galp) to UDP- Formation of N5-adducts in non-redox reactions involving the galactofuranose (UDP-Galf) by UDP-galactopyranose mutase flavin in the oxidized or reduced forms have also recently been (UGM). The role of the reduced flavin in the non-redox reaction demonstrated. In the reaction of alkyl-dihydroxyacetone phosphate catalyzed by UGM is the focus of this review. We will discuss recent synthase (ADPS), the substrate attacks the N5-atom of the oxidized biochemical, structural, and computational data that suggest that flavin, and formation of the N5-iminum ion facilitates elimination the flavin cofactor in UGM plays multiple roles in catalysis. We will of the fatty acid. Formation of the N5-iminium ion activates the C1- focus on the mechanism of activation of the flavin-N5 for covalent atom, which is attacked by the fatty alcohol (e.g., Nu: in Scheme 2) catalysis, the role of the oxygen atom at the C4 positon (C4O) in [29,30]. In the ADPS reaction, the substrate functions as a nucleo- proton transfer and activation of flavin-sugar intermediates, and of phile and attacks the N5-atom of the flavin, which functions as an the 20-OH of the ribityl chain in stabilization of conformational electrophile. changes that modulate bending of the reduced flavin, which is In the reaction catalyzed by UGM (Scheme 3), the flavin is essential for the proton transfer function of the C4O. required to be in the reduced state and functions as a nucleophile. In this reaction, the substrate is not activated for N5-adduct Scheme 1. Structure of the isoalloxazine ring highlighting hot spots for covalent catalysis. (A) Hot spots of the 2-electron reduced flavin. Molecular oxygen is activated and form a covalent intermediate at the C4a position in monooxygenases. The N5-atom functions as a nucleophile attacking the C1-atom of UDP-Galp in UGM. (B) Hot spots of the
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